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test_convenient_superpose.py

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    • user avatar
    removed import of geom,io,mol,seq,gfx and img from ost base __init__.py
    Andreas Schenk authored 
    changed python unit tests to run with python instead of ost

Remarks
-------

Python unit tests using blast, clustalw or the compound lib where
skipped on my system. There might be still some missing imports in
these tests.
    75c977b5
    History
    user avatar 75c977b5
    History
    test_convenient_superpose.py 9.21 KiB
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    from ost import io,mol,geom
import unittest
import os
import random

class TestConvenientSuperpose(unittest.TestCase):
  
  def setUp(self):
    pass
  
  def assertEqualAtomOrder(self, view1, view2):
    self.assertEquals(len(view1.atoms),len(view2.atoms))
    for a1, a2 in zip(view1.atoms, view2.atoms):
      self.assertEquals(a1.element, a2.element)
      self.assertTrue(geom.Equal(a1.pos, a2.pos))

  def testAssertion(self):
    ent1_ent = io.LoadEntity(os.path.join("testfiles","1aho.pdb"))
    ent1_view = ent1_ent.Select("")
    self.assertEqualAtomOrder(ent1_ent, ent1_ent)
    self.assertEqualAtomOrder(ent1_ent, ent1_view)
    self.assertEqualAtomOrder(ent1_view, ent1_ent)
    self.assertEqualAtomOrder(ent1_view, ent1_view)
    self.assertRaises(AssertionError, self.assertEqualAtomOrder, ent1_view.Select("ele!=H"), ent1_view)
    
  def testCorrectlyOrdered(self):
    ent1_ent = io.LoadEntity(os.path.join("testfiles","1aho.pdb"))
    ent1_view = ent1_ent.Select("")
    ## test MatchResidueByNum
    view1, view2 = mol.alg.MatchResidueByNum(ent1_ent, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent1_view, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent1_ent, ent1_view)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent1_view, ent1_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByIdx
    view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByIdx(ent1_view, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByIdx(ent1_ent, ent1_view)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByIdx(ent1_view, ent1_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByGlobalAln
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_ent, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_view, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_ent, ent1_view)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent1_view, ent1_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByLocalAln
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_ent, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_view, ent1_ent)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_ent, ent1_view)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent1_view, ent1_view)
    self.assertEqualAtomOrder(view1, view2)

  def testMissingFirstAtom(self):
    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
    ent_view_missing = ent_view.Select("not (cname=A and rnum=1 and aname=N)")
    ## test MatchResidueByNum
    view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByIdx
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByGlobalAln
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByLocalAln
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)

  def testMissingManyAtoms(self):
    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
    ent_view_missing = ent_view.Select("not (cname=A and rnum=3,19,32 and aname=CB,CA,CD)")
    ## test MatchResidueByNum
    view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByIdx
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByGlobalAln
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByLocalAln
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)

  def testMissingFirstResidue(self):
    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
    ent_view_missing = ent_view.Select("not (cname=A and rnum=1)")
    ## test MatchResidueByNum
    view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByGlobalAln
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByLocalAln
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)

  def testMissingHydrogens(self):
    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
    ent_view_missing = ent_view.Select("ele!=H")
    ## test MatchResidueByNum
    view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByIdx
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_missing)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view_missing, ent_view)
    self.assertEqualAtomOrder(view1, view2)
  
  def testWrongAtomOrder(self):
    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
    ent_view_wrong = ent_view.CreateEmptyView()
    for c in ent_view.chains:
      ent_view_wrong.AddChain(c)
      for r in c.residues:
        ent_view_wrong.AddResidue(r)
        atoms = list(r.atoms)
        random.shuffle(atoms)
        for a in atoms:
          ent_view_wrong.AddAtom(a)
    ## test MatchResidueByNum
    view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_wrong)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent_view_wrong, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByIdx
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view, ent_view_wrong)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByIdx(ent_view_wrong, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByGlobalAln
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view, ent_view_wrong)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByGlobalAln(ent_view_wrong, ent_view)
    self.assertEqualAtomOrder(view1, view2)
    ## test MatchResidueByLocalAln
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view, ent_view_wrong)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByLocalAln(ent_view_wrong, ent_view)
    self.assertEqualAtomOrder(view1, view2)

  def testWrongResidueOrder(self): 
    ent_view = io.LoadEntity(os.path.join("testfiles","1aho.pdb")).Select("")
    ent_view_wrong = ent_view.CreateEmptyView()
    for c in ent_view.chains:
      ent_view_wrong.AddChain(c)
      residues = list(c.residues)
      random.shuffle(residues)
      for r in residues:
        ent_view_wrong.AddResidue(r)
        for a in r.atoms:
          av=ent_view_wrong.AddAtom(a)
    ## test MatchResidueByNum
    view1, view2 = mol.alg.MatchResidueByNum(ent_view, ent_view_wrong)
    self.assertEqualAtomOrder(view1, view2)
    view1, view2 = mol.alg.MatchResidueByNum(ent_view_wrong, ent_view)
    self.assertEqualAtomOrder(view1, view2)

if __name__ == "__main__":
  from ost import testutils
  testutils.RunTests()